A two-step probing method to compare lysine accessibility across macromolecular complex conformations

Author(s)

MacRae, Andrew J. ^{[1, 2]} ; Coltri, Patricia ^{[3, 1]} ; Hrabeta-Robinson, Eva ^[1] ; Chalkley, Robert J. ^[4] ; Burlingame, A. L. ^[4] ; Jurica, Melissa S. ^{[1, 2]}

Affiliation

^[1] Univ Calif Santa Cruz, Dept Mol Cell & Dev Biol, Santa Cruz, CA 95064 - USA

^[2] Univ Calif Santa Cruz, Ctr Mol Biol RNA, Santa Cruz, CA 95064 - USA

^[3] Univ Sao Paulo, Dept Cell & Dev Biol, Sao Paulo - Brazil

^[4] Univ Calif San Francisco, Dept Pharmaceut Chem, San Francisco, CA 94143 - USA

• Document type: Journal article
• Source: RNA BIOLOGY; v. 16, n. 10 JUN 2019.
• Web of Science Citations: 0

Abstract

Structural models of large and dynamic molecular complexes are appearing in increasing numbers, in large part because of recent technical advances in cryo-electron microscopy. However, the inherent complexity of such biological assemblies comprising dozens of moving parts often limits the resolution of structural models and leaves the puzzle as to how each functional configuration transitions to the next. Orthogonal biochemical information is crucial to understanding the molecular interactions that drive those rearrangements. We present a two-step method for chemical probing detected by tandem mass-spectrometry to globally assess the reactivity of lysine residues within purified macromolecular complexes. Because lysine side chains often balance the negative charge of RNA in ribonucleoprotein complexes, the method is especially useful for detecting changes in protein-RNA interactions. By probing the E. coli 30S ribosome subunit, we established that the reactivity pattern of lysine residues quantitatively reflects structure models derived from X-ray crystallography. We also used the strategy to assess differences in three conformations of purified human spliceosomes in the context of recent cryo-electron microscopy models. Our results demonstrate that the probing method yields powerful biochemical information that helps contextualize architectural rearrangements of intermediate resolution structures of macromolecular complexes, often solved in multiple conformations. (AU)

• FAPESP's process: 17/06994-9 - MicroRNA splicing regulation in eukaryotes
• Grantee: Patricia Pereira Coltri
• Support Opportunities: Regular Research Grants